Mercurial > repos > iuc > mothur_dist_shared
comparison dist.shared.xml @ 2:b7da1494afa1 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
author | iuc |
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date | Tue, 20 Mar 2018 22:11:03 -0400 |
parents | 7773b7afb53d |
children | 418100660ba3 |
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1:bba3c4af4982 | 2:b7da1494afa1 |
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5 </macros> | 5 </macros> |
6 <expand macro="requirements"/> | 6 <expand macro="requirements"/> |
7 <expand macro="stdio"/> | 7 <expand macro="stdio"/> |
8 <expand macro="version_command"/> | 8 <expand macro="version_command"/> |
9 <command><![CDATA[ | 9 <command><![CDATA[ |
10 @SHELL_OPTIONS@ | 10 @SHELL_OPTIONS@ |
11 | 11 |
12 ## create symlinks to input datasets | 12 ## create symlinks to input datasets |
13 ln -s "$otu" otu.dat && | 13 ln -s '$otu' otu.dat && |
14 | 14 |
15 echo 'dist.shared( | 15 echo 'dist.shared( |
16 shared=otu.dat, | 16 shared=otu.dat, |
17 #if $label: | 17 #if $label: |
18 label=${ str($label).replace(",","-") }, | 18 label=${ str($label).replace(",","-") }, |
19 #end if | 19 #end if |
20 #if $groups: | 20 #if $groups: |
21 groups=${ str($groups).replace(",","-") }, | 21 groups=${ str($groups).replace(",","-") }, |
22 #end if | 22 #end if |
23 #if $calc: | 23 #if $calc: |
24 calc=${ str($calc).replace(",","-") }, | 24 calc=${ str($calc).replace(",","-") }, |
25 #end if | 25 #end if |
26 #if $subsampling.use == "yes": | 26 #if $subsampling.use == "yes": |
27 #if $subsampling.subsample: | 27 #if $subsampling.subsample: |
28 subsample=$subsampling.subsample, | 28 subsample=$subsampling.subsample, |
29 #end if | 29 #else |
30 iters=$subsampling.iters, | 30 subsample=T, |
31 #end if | 31 #end if |
32 output=$output, | 32 iters=$subsampling.iters, |
33 processors='\${GALAXY_SLOTS:-8}' | 33 #end if |
34 )' | 34 output=$output, |
35 | sed 's/ //g' ## mothur trips over whitespace | 35 processors='\${GALAXY_SLOTS:-8}' |
36 | mothur | 36 )' |
37 | tee mothur.out.log | 37 | sed 's/ //g' ## mothur trips over whitespace |
38 | mothur | |
39 | tee mothur.out.log | |
38 ]]></command> | 40 ]]></command> |
39 <inputs> | 41 <inputs> |
40 <param name="otu" type="data" format="mothur.shared" label="shared - OTU Shared"/> | 42 <param name="otu" type="data" format="mothur.shared" label="shared - OTU Shared"/> |
41 <param name="label" type="select" label="label - OTU Labels to calculate" multiple="true"> | 43 <param name="label" type="select" label="label - OTU Labels to calculate" multiple="true"> |
42 <expand macro="labeloptions"/> | 44 <expand macro="labeloptions"/> |
56 <param name="use" type="select" label="subsample"> | 58 <param name="use" type="select" label="subsample"> |
57 <option value="no" selected="true">no</option> | 59 <option value="no" selected="true">no</option> |
58 <option value="yes">yes</option> | 60 <option value="yes">yes</option> |
59 </param> | 61 </param> |
60 <when value="yes"> | 62 <when value="yes"> |
61 <param name="subsample" type="integer" value="" min="0" optional="true" label="subsample (defaults to the size of the smallest group)" help="Should not exceed the number of sequences in any group"/> | 63 <param name="subsample" type="integer" value="" min="0" optional="true" label="subsample (defaults to the size of the smallest group)" |
64 help="Should not exceed the number of sequences in any group"/> | |
62 <param name="iters" type="integer" value="1000" min="1" optional="true" label="iters - Number of iterations to try (default 1000)"/> | 65 <param name="iters" type="integer" value="1000" min="1" optional="true" label="iters - Number of iterations to try (default 1000)"/> |
63 </when> | 66 </when> |
64 <when value="no"/> | 67 <when value="no"/> |
65 </conditional> | 68 </conditional> |
66 <param name="output" type="select" label="output - Distance Matrix Output Format" help="A Distance Matrix will be generated for each calculator label pair"> | 69 <param name="output" type="select" label="output - Distance Matrix Output Format" help="A Distance Matrix will be generated for each calculator label pair"> |
67 <option value="lt" selected="true">Phylip formatted Lower Triangle Matrix</option> | 70 <option value="lt" selected="true">Phylip formatted Lower Triangle Matrix</option> |
68 <option value="square">Phylip formatted Square Matrix</option> | 71 <option value="square">Phylip formatted Square Matrix</option> |
69 </param> | 72 </param> |
73 <expand macro="param-savelog"/> | |
70 </inputs> | 74 </inputs> |
71 <outputs> | 75 <outputs> |
72 <expand macro="logfile-output"/> | 76 <expand macro="logfile-output"/> |
73 <collection name="distfiles" type="list" label="${tool.name} on ${on_string}: dist files"> | 77 <collection name="distfiles" type="list" label="${tool.name} on ${on_string}: dist files"> |
74 <discover_datasets pattern=".*?\.(?P<designation>.*)\.dist" format="mothur.dist"/> | 78 <discover_datasets pattern=".*?\.(?P<designation>.*)\.dist" format="mothur.dist"/> |
78 <test><!-- test with defaults --> | 82 <test><!-- test with defaults --> |
79 <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/> | 83 <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/> |
80 <output_collection name="distfiles" count="72"> | 84 <output_collection name="distfiles" count="72"> |
81 <element name="thetayc.0.33.lt" md5="c707e43f14c2022f4027e6a2495cbae8" ftype="mothur.dist"/> | 85 <element name="thetayc.0.33.lt" md5="c707e43f14c2022f4027e6a2495cbae8" ftype="mothur.dist"/> |
82 </output_collection> | 86 </output_collection> |
87 <param name="savelog" value="true"/> | |
83 <expand macro="logfile-test"/> | 88 <expand macro="logfile-test"/> |
84 </test> | 89 </test> |
85 <test><!-- test with label,group select and all calculators --> | 90 <test><!-- test with label,group select and all calculators --> |
86 <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/> | 91 <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/> |
87 <param name="label" value="0.05,0.22"/> | 92 <param name="label" value="0.05,0.22"/> |
88 <param name="groups" value="forest,pasture"/> | 93 <param name="groups" value="forest,pasture"/> |
89 <param name="calc" value="sharedsobs,sharedchao,sharedace,anderberg,jclass,jest,kulczynski,kulczynskicody,kstest,lennon,ochiai,sorclass,sorest,whittaker,hamming,memchi2,memchord,memeuclidean,mempearson,braycurtis,jabund,morisitahorn,sorabund,thetan,thetayc,canberra,gower,hellinger,manhattan,odum,soergel,spearman,speciesprofile,structchi2,structeuclidean,structpearson,sharednseqs,sharedobserved"/> | 94 <param name="calc" value="sharedsobs,sharedchao,sharedace,anderberg,jclass,jest,kulczynski,kulczynskicody,kstest,lennon,ochiai,sorclass,sorest,whittaker,hamming,memchi2,memchord,memeuclidean,mempearson,braycurtis,jabund,morisitahorn,sorabund,thetan,thetayc,canberra,gower,hellinger,manhattan,odum,soergel,spearman,speciesprofile,structchi2,structeuclidean,structpearson,sharednseqs,sharedobserved"/> |
90 <output_collection name="distfiles" count="74"> | 95 <output_collection name="distfiles" count="74"> |
91 <element name="gower.0.22.lt" md5="209dbf7e9f1e13753524905f64c8e3b7" ftype="mothur.dist"/> | 96 <element name="gower.0.22.lt" md5="209dbf7e9f1e13753524905f64c8e3b7" ftype="mothur.dist"/> |
92 </output_collection> | 97 </output_collection> |
98 <param name="savelog" value="true"/> | |
93 <expand macro="logfile-test"/> | 99 <expand macro="logfile-test"/> |
94 </test> | 100 </test> |
95 <test><!-- test with subsampling --> | 101 <test><!-- test with subsampling without specifying size --> |
96 <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/> | 102 <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/> |
103 <param name="label" value="0.03,0.33"/> | |
97 <param name="use" value="yes"/> | 104 <param name="use" value="yes"/> |
98 <param name="subsample" value="10"/> | |
99 <param name="iters" value="42"/> | |
100 <param name="label" value="0.03,0.33"/> | |
101 <param name="calc" value="canberra"/> | 105 <param name="calc" value="canberra"/> |
102 <param name="output" value="square"/> | 106 <param name="output" value="square"/> |
103 <output_collection name="distfiles" count="6"> | 107 <output_collection name="distfiles" count="6"> |
104 <element name="canberra.0.33.square.std" ftype="mothur.dist"> | 108 <element name="canberra.0.33.square.std" ftype="mothur.dist"> |
105 <assert_contents> | 109 <assert_contents> |
106 <has_text text="forest"/> | 110 <has_text text="forest"/> |
107 <has_text text="pasture"/> | 111 <has_text text="pasture"/> |
108 </assert_contents> | 112 </assert_contents> |
109 </element> | 113 </element> |
110 </output_collection> | 114 </output_collection> |
115 <param name="savelog" value="true"/> | |
116 <expand macro="logfile-test"/> | |
117 </test> | |
118 <test><!-- test with subsampling with specifying size--> | |
119 <param name="otu" value="amazon.mothur.shared" ftype="mothur.shared"/> | |
120 <param name="use" value="yes"/> | |
121 <param name="subsample" value="2"/> | |
122 <param name="iters" value="42"/> | |
123 <param name="label" value="0.10"/> | |
124 <param name="calc" value="canberra"/> | |
125 <param name="output" value="square"/> | |
126 <output_collection name="distfiles" count="3"> | |
127 <element name="canberra.0.10.square.std" ftype="mothur.dist"> | |
128 <assert_contents> | |
129 <has_text text="forest"/> | |
130 <has_text text="pasture"/> | |
131 </assert_contents> | |
132 </element> | |
133 </output_collection> | |
134 <param name="savelog" value="true"/> | |
111 <expand macro="logfile-test"/> | 135 <expand macro="logfile-test"/> |
112 </test> | 136 </test> |
113 </tests> | 137 </tests> |
114 <help> | 138 <help><![CDATA[ |
115 <![CDATA[ | |
116 | 139 |
117 @MOTHUR_OVERVIEW@ | 140 @MOTHUR_OVERVIEW@ |
118 | 141 |
119 **Command Documentation** | 142 **Command Documentation** |
120 | 143 |
124 .. _shared: https://www.mothur.org/wiki/Shared_file | 147 .. _shared: https://www.mothur.org/wiki/Shared_file |
125 .. _dist.shared: https://www.mothur.org/wiki/Dist.shared | 148 .. _dist.shared: https://www.mothur.org/wiki/Dist.shared |
126 | 149 |
127 v1.26.0: Updated to Mothur 1.33. Omitted calculators since they do not appear to be available. | 150 v1.26.0: Updated to Mothur 1.33. Omitted calculators since they do not appear to be available. |
128 | 151 |
129 ]]> | 152 ]]></help> |
130 </help> | |
131 <expand macro="citations"/> | 153 <expand macro="citations"/> |
132 </tool> | 154 </tool> |